Man pages for kgori/sigfit
Flexible Bayesian inference of mutational signatures
| build_catalogues | Build mutational catalogues |
| build_opps_matrix | Build an opportunities matrix |
| calculate_gof | Do goodness-of-fit calculations |
| convert_signatures | Convert signatures between models |
| cosine_sim | Cosine similarity between two vectors |
| cosmic_signatures_doublet_v3.2 | Doublet base substitution signatures from COSMIC v3.2 |
| cosmic_signatures_indel_v3.2 | Small insertion/deletion signatures from COSMIC v3.2 |
| cosmic_signatures_strand_v3 | Single base substitution signatures from COSMIC v3 with... |
| cosmic_signatures_v2 | Single base substitution signatures from COSMIC v2 |
| cosmic_signatures_v3 | Single base substitution signatures from COSMIC v3 |
| cosmic_signatures_v3.2 | Single base substitution signatures from COSMIC v3.2 |
| default_sig_palette | Generate default colour palette for signatures |
| extract_signatures | Extract mutational signatures |
| extract_signatures_initialiser | Use optimization to generate initial parameter values for... |
| fetch_cosmic_data | Fetch COSMIC mutational signatures (DEPRECATED) |
| fit_extract_signatures | Fit-and-extract mutational signatures |
| fit_signatures | Fit mutational signatures |
| get_initializer_list | Query a signature extraction result for parameter values that... |
| get_loglik | Generate log likelihood values from a model |
| get_reconstructions | Generate reconstructed mutation catalogues from parameters... |
| human_trinuc_freqs | Retrieve human trinucleotide frequencies |
| l2_norm | L2 norm between two vectors |
| letterwrap | From https://stackoverflow.com/a/21689613/1875814 Produce... |
| make_colors | Colour warnings for posterior predictive checks yellow =... |
| match_signatures | Find the best matches between two sets of signatures |
| mut_types | Generates character vector of 96 (or 192, if strand=TRUE)... |
| plot_all | Plot all results from signature fitting or extraction |
| plot_exposures | Plot signature exposures |
| plot_gof | Plot goodness-of-fit |
| plot_ppc | Plot result of posterior predictive check |
| plot_reconstruction | Plot mutational spectrum reconstructions |
| plot_spectrum | Plot mutational spectra |
| plot_spectrum_dbs | Plot DBS (doublet) spectrum |
| plot_spectrum_generic | Plot generic spectrum |
| plot_spectrum_id | Plot ID (indel) spectrum |
| plot_spectrum_sbs | Plot SBS spectrum |
| plot_spectrum_tsw | Plot strandwise SBS spectrum |
| remove_zeros_ | Deal with zero values in a signature |
| retrieve_pars | Retrieve model parameters |
| rev_comp | Reverse complement a nucleotide sequence string Input is... |
| sigfit-package | sigfit: flexible Bayesian inference of mutational signatures |
| simulate_ppc | Generate posterior predictive check values from a model |
| stan_models | Access stan models |
| to_matrix | Initial coercion to matrix for signatures/exposures/counts |
